[gmx-users] Genion

Thu Jun 22 13:34:42 CEST 2017

Hi, the procedure as defined by Juistin worked out well. However, a new problem has occurred. At mdrun for the minimization, I get: 

------------------------------------------------------- 
Program gmx mdrun, VERSION 5.1.2 
Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, line: 276 

Fatal error: 
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. 
This usually means that your system is not well equilibrated. 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 

This may be caused by the solvent replacement of genion by Na Cl: 

Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
Will try to add 130 Na ions and 90 Cl ions. 
Select a continuous group of solvent molecules 
Group 0 ( System) has 98254 elements 
Group 1 ( DNA) has 1333 elements 
Group 2 ( Water) has 96921 elements 
Group 3 ( SOL) has 96921 elements 
Group 4 ( non-Water) has 1333 elements 
Select a group: 3 
Selected 3: 'SOL' 
Number of (3-atomic) solvent molecules: 32307 
Replacing solvent molecule 3244 (atom 11065) with Na 
Replacing solvent molecule 8993 (atom 28312) with Na 
Replacing solvent molecule 7088 (atom 22597) with Na 
Replacing solvent molecule 29442 (atom 89659) with Na 
Replacing solvent molecule 30079 (atom 91570) with Na 
Replacing solvent molecule 5128 (atom 16717) with Na 
Replacing solvent molecule 10705 (atom 33448) with Na 
Replacing solvent molecule 1418 (atom 5587) with Na 
Replacing solvent molecule 6608 (atom 21157) with Na 
Replacing solvent molecule 28124 (atom 85705) with Na 
Replacing solvent molecule 5440 (atom 17653) with Na 
Replacing solvent molecule 31518 (atom 95887) with Na 
Replacing solvent molecule 16384 (atom 50485) with Na 
Replacing solvent molecule 17675 (atom 54358) with Na 
Replacing solvent molecule 23446 (atom 71671) with Na 
Replacing solvent molecule 15659 (atom 48310) with Na 
Replacing solvent molecule 18442 (atom 56659) with Na 
Replacing solvent molecule 23777 (atom 72664) with Na 
Replacing solvent molecule 5965 (atom 19228) with Na 
Replacing solvent molecule 15375 (atom 47458) with Na 
Replacing solvent molecule 30985 (atom 94288) with Na 
Replacing solvent molecule 19076 (atom 58561) with Na 
Replacing solvent molecule 18065 (atom 55528) with Na 
Replacing solvent molecule 22711 (atom 69466) with Na 
Replacing solvent molecule 27097 (atom 82624) with Na 
Replacing solvent molecule 21561 (atom 66016) with Na 
Replacing solvent molecule 18592 (atom 57109) with Na 
Replacing solvent molecule 22174 (atom 67855) with Na 
Replacing solvent molecule 17888 (atom 54997) with Na 
Replacing solvent molecule 13005 (atom 40348) with Na 
Replacing solvent molecule 3481 (atom 11776) with Na 
Replacing solvent molecule 22603 (atom 69142) with Na 
Replacing solvent molecule 9899 (atom 31030) with Na 
Replacing solvent molecule 3438 (atom 11647) with Na 
Replacing solvent molecule 12180 (atom 37873) with Na 
Replacing solvent molecule 32219 (atom 97990) with Na 
Replacing solvent molecule 23159 (atom 70810) with Na 
Replacing solvent molecule 27929 (atom 85120) with Na.... 

which then reflects on grompp as: 

Setting the LD random seed to 3274024379 
Generated 2211 of the 2211 non-bonded parameter combinations 
Generating 1-4 interactions: fudge = 0.5 
Generated 2211 of the 2211 1-4 parameter combinations 
Excluding 3 bonded neighbours molecule type 'DNA_chain_E' 
Excluding 3 bonded neighbours molecule type 'DNA_chain_F' 
Excluding 2 bonded neighbours molecule type 'SOL' 
Excluding 1 bonded neighbours molecule type 'NA' 
Excluding 1 bonded neighbours molecule type 'CL' 
Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97608 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97609 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97610 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97611 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97612 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97613 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
Warning: atom name 97614 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) 
(more than 20 non-matching atom names) 

WARNING 1 [file topol.top, line 50]: 
220 non-matching atom names 
atom names from topol.top will be used 
atom names from dna_solv_NaCl.gro will be ignored 

Giving the mdrun problem.. 

Not sure how to get by this! 

Sergio 

Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Wednesday, June 21, 2017 4:53:59 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:45 AM, Sergio Manzetti wrote: 
> Hi Justin, the sequence was: 
> 
> gmx editconf .... 
> 
> gmx solvate .... 
> 
> gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 
> 
> gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL 
> 
> then: 
> 
> gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM 
> 
> gmx mdrun 
> 
> 
> This worked. 
> 
> Then for the sim: 
> 
> dna_solv_NaCl_EM.gro does not contain any ions. 
> 

You didn't pass topol_solvated.top to genion -p, so it did not update the number 
of ions. Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually. But again, 
it is *impossible* for mdrun to delete anything. So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have. 

-Justin 

-- 
================================================== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

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